org.jmol.adapter.readers.xtal
Class CastepReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.xtal.CastepReader
public class CastepReader
- extends AtomSetCollectionReader
CASTEP (http://www.castep.org) .cell file format
relevant section of .cell file are included as comments below
- Version:
- 1.2
- Author:
- Joerg Meyer, FHI Berlin 2009 (meyer@fhi-berlin.mpg.de)
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
tokens
private java.lang.String[] tokens
a
private float a
b
private float b
c
private float c
alpha
private float alpha
beta
private float beta
gamma
private float gamma
abc
private javax.vecmath.Vector3f[] abc
iHaveFractionalCoordinates
private boolean iHaveFractionalCoordinates
lengthUnitIds
private static final java.lang.String[] lengthUnitIds
lengthUnitFactors
private static final float[] lengthUnitFactors
lengthUnits
private static final int lengthUnits
CastepReader
public CastepReader()
initializeReader
public void initializeReader()
throws java.lang.Exception
- Overrides:
initializeReader
in class AtomSetCollectionReader
- Throws:
java.lang.Exception
finalizeReader
protected void finalizeReader()
throws java.lang.Exception
- Overrides:
finalizeReader
in class AtomSetCollectionReader
- Throws:
java.lang.Exception
readLatticeAbc
private void readLatticeAbc()
throws java.lang.Exception
- Throws:
java.lang.Exception
readLatticeCart
private void readLatticeCart()
throws java.lang.Exception
- Throws:
java.lang.Exception
readPositionsFrac
private void readPositionsFrac()
throws java.lang.Exception
- Throws:
java.lang.Exception
readPositionsAbs
private void readPositionsAbs()
throws java.lang.Exception
- Throws:
java.lang.Exception
readLengthUnit
private float readLengthUnit()
throws java.lang.Exception
- Throws:
java.lang.Exception
readAtomData
private void readAtomData(float factor)
throws java.lang.Exception
- Throws:
java.lang.Exception
tokenizeCastepCell
private int tokenizeCastepCell()
throws java.lang.Exception
- Throws:
java.lang.Exception